Blender getting very slow in handling large data?
The answer to the question you asked is that 54000 individual objects is significantly different from 54000 polygons, so it's not surprising that Blender is having trouble with that many individual objects. There are some ways to improve viewport performance like turning on VBOs in the user preferences, but I don't think any of them will be terribly helpful at this point.

If all the planes were joined into one object, it'd probably perform much better, but it doesn't seem like that would be very helpful, for what you're doing.

The answer to the question you didn't ask ;-) is that this is a really expensive way to render a point cloud in Blender. There are two tools that will probably be very useful to you. One will get point clouds into Blender, and the other will skin point clouds in Blender. And this will probably be much more workable than your current solution ;-)

Hope that helps!